One of input files can be paired to multiple files

[mbk0asis]

Hi, I have paired fastq files for 60 samples in a directory "TRIMMED", then I ran

SalmonTE.py quant --reference=mm TRIMMED/

I got following error.

2020-06-12 18:58:43,344 Starting quantification mode
2020-06-12 18:58:43,344 Collecting FASTQ files...
2020-06-12 18:58:43,344 SalmonTE assumes that 'TRIMMED/' is a directory, and SalmonTE will search any FASTQ file in the directory.
2020-06-12 18:58:44,711 One of input files can be paired to multiple files

Fastq file names are like these

muscle14f1_R1.fq.gz
muscle14f1_R2.fq.gz

muscle14f2_R1.fq.gz
muscle14f2_R2.fq.gz

I remove any delimiter in the sample name just in case file name cause a bug. What could be the problem here?

Thank you~

[hyunhwan-jeong]

Thanks for reporting this. It would be helpful if you print the first line of each file of fastq files to resolve the problem.

Best,

Hyun-Hwan Jeong